6db8 - Revision history

OCA at 15:21, 4 October 2023

OCA — Wed, 04 Oct 2023 15:21:14 GMT

←Older revision		Revision as of 15:21, 4 October 2023
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	<StructureSection load='6db8' size='340' side='right'caption='[[6db8]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='6db8' size='340' side='right'caption='[[6db8]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6db8]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DB8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6db8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DB8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G4A:2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium'>G4A</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8654134Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db8 OCA], [~~http~~://pdbe.org/6db8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6db8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6db8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6db8 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G4A:2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium'>G4A</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db8 OCA], [https://pdbe.org/6db8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6db8 RCSB], [https://www.ebi.ac.uk/pdbsum/6db8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6db8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Laski, A]]	+	[[Category: Laski A]]
-	[[Category: Piccirilli~~, J A~~]]	+	[[Category: Piccirilli JA]]
-	[[Category: Shao, Y]]	+	[[Category: Shao Y]]
-	[[Category: Shelke~~, S A]]~~	+	[[Category: Shelke SA]]
-	~~[[Category: Dir]]~~	+
-	~~[[Category: Fab]]~~	+
-	~~[[Category: Fluorescent aptamer]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna-immune system complex~~]]	+

OCA at 10:03, 18 December 2019

OCA — Wed, 18 Dec 2019 10:03:25 GMT

←Older revision		Revision as of 10:03, 18 December 2019
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	==Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer==		==Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer==
-	<StructureSection load='6db8' size='340' side='right' caption='[[6db8]], [[Resolution\|resolution]] 1.87Å' scene=''>	+	<StructureSection load='6db8' size='340' side='right'caption='[[6db8]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6db8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6db8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G4A:2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium'>G4A</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G4A:2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium'>G4A</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db8 OCA], [http://pdbe.org/6db8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db8 RCSB], [http://www.ebi.ac.uk/pdbsum/6db8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db8 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db8 OCA], [http://pdbe.org/6db8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db8 RCSB], [http://www.ebi.ac.uk/pdbsum/6db8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db8 ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Laski, A]]		[[Category: Laski, A]]
	[[Category: Piccirilli, J A]]		[[Category: Piccirilli, J A]]

OCA at 08:14, 14 November 2018

OCA — Wed, 14 Nov 2018 08:14:59 GMT

←Older revision		Revision as of 08:14, 14 November 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6db8 is ~~ON HOLD until Paper~~ Publication	+	==Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer==
		+	<StructureSection load='6db8' size='340' side='right' caption='[[6db8]], [[Resolution\|resolution]] 1.87Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6db8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G4A:2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium'>G4A</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db8 OCA], [http://pdbe.org/6db8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db8 RCSB], [http://www.ebi.ac.uk/pdbsum/6db8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db8 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO3 bound forms of DIR2s at 2.0 A and 1.8 A resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure.

-	~~Authors: Shao, Y~~., Shelke, ~~S.A.~~, Laski, A., ~~Piccirilli~~, J.A.	+	Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.,Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA Nat Commun. 2018 Oct 31;9(1):4542. doi: 10.1038/s41467-018-06942-3. PMID:30382099<ref>PMID:30382099</ref>

-	~~Description: Structural basis for promiscuous binding and activation~~ of ~~fluorogenic dyes by DIR2s RNA aptamer~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Shelke, S.A]]~~	+	<div class="pdbe-citations 6db8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Laski, A]]		[[Category: Laski, A]]
		+	[[Category: Piccirilli, J A]]
	[[Category: Shao, Y]]		[[Category: Shao, Y]]
-	[[Category: ~~Piccirilli~~, J.A]]	+	[[Category: Shelke, S A]]
		+	[[Category: Dir]]
		+	[[Category: Fab]]
		+	[[Category: Fluorescent aptamer]]
		+	[[Category: Rna]]
		+	[[Category: Rna-immune system complex]]

OCA at 05:34, 14 June 2018

OCA — Thu, 14 Jun 2018 05:34:39 GMT

←Older revision		Revision as of 05:34, 14 June 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6db8 is ON HOLD	+	The entry 6db8 is ON HOLD until Paper Publication

	Authors: Shao, Y., Shelke, S.A., Laski, A., Piccirilli, J.A.		Authors: Shao, Y., Shelke, S.A., Laski, A., Piccirilli, J.A.

OCA at 04:15, 6 June 2018

OCA — Wed, 06 Jun 2018 04:15:14 GMT

←Older revision		Revision as of 04:15, 6 June 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6db8 is ON HOLD ~~until sometime in the future~~	+	The entry 6db8 is ON HOLD

-	Authors: Shao, Y., Shelke, S.A., ~~Lask~~, A., Piccirilli, J.A.	+	Authors: Shao, Y., Shelke, S.A., Laski, A., Piccirilli, J.A.

	Description: Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer		Description: Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Shelke, S.A]]		[[Category: Shelke, S.A]]
		+	[[Category: Laski, A]]
	[[Category: Shao, Y]]		[[Category: Shao, Y]]
-	[[Category: Lask, A]]
	[[Category: Piccirilli, J.A]]		[[Category: Piccirilli, J.A]]

OCA at 04:03, 16 May 2018

OCA — Wed, 16 May 2018 04:03:41 GMT

←Older revision		Revision as of 04:03, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6db8 is ON HOLD	+	The entry 6db8 is ON HOLD until sometime in the future

	Authors: Shao, Y., Shelke, S.A., Lask, A., Piccirilli, J.A.		Authors: Shao, Y., Shelke, S.A., Lask, A., Piccirilli, J.A.

OCA: Protected "6db8" [edit=sysop:move=sysop]

OCA — Wed, 09 May 2018 04:57:32 GMT

Protected "6db8" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:57, 9 May 2018

OCA: New page: '''Unreleased structure''' The entry 6db8 is ON HOLD Authors: Shao, Y., Shelke, S.A., Lask, A., Piccirilli, J.A. Description: Structural basis for promiscuous binding and activation of...

OCA — Wed, 09 May 2018 04:57:30 GMT

New page: '''Unreleased structure''' The entry 6db8 is ON HOLD Authors: Shao, Y., Shelke, S.A., Lask, A., Piccirilli, J.A. Description: Structural basis for promiscuous binding and activation of...

New page

'''Unreleased structure'''

The entry 6db8 is ON HOLD

Authors: Shao, Y., Shelke, S.A., Lask, A., Piccirilli, J.A.

Description: Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer
[[Category: Unreleased Structures]]
[[Category: Shelke, S.A]]
[[Category: Shao, Y]]
[[Category: Lask, A]]
[[Category: Piccirilli, J.A]]